Sulfur isotope fractionation during microbial sulfate reduction in brackish estuarine sediments was studied using an experimental flow-through reactor approach designed to preserve the in situ physical, geochemical and microbial structure of the sediment. Concurrent measurements of potential sulfate reduction rates and 34S/32S fractionations were carried out using intact sediment slices (2 cm thick, 4.2 cm diameter) from unvegetated, intertidal sites adjoining a salt marsh along the Scheldt estuary, The Netherlands. A total of 30 reactor experiments were performed with sediments collected in February, May and October 2006. The effects of incubation temperature (10, 20, 30 and 50 °C) and sediment depth (0–2, 4–6 and 8–10 cm) were investigated. Sulfate was supplied in non-limiting concentrations via the reactor inflow solutions; no external electron donor was supplied. Isotope fractionations (e values) were calculated from the measured differences in sulfate d34S between in- and outflow solutions of the reactors, under quasi-steady state conditions. Potential sulfate reduction rates (SRR) varied over one order of magnitude (5–49 nmol cm-3 h-1) and were highest in the 30 °C incubations. They decreased systematically with depth, and were highest in the sediments collected closest to the vegetated marsh. Isotope fractionations ranged from 9‰ to 34‰ and correlated inversely with SRR, as predicted by the standard fractionation model for enzymatic sulfate reduction of Rees (1973). The e versus SRR relationship, however, varied between sampling times, with higher e values measured in February, at comparable SRRs, than in May and October. The observed e versus SRR relationships also deviated from the previously reported inverse trend for sediments collected in a marine lagoon in Denmark (Canfield, 2001b). Thus, isotope fractionation during sulfate reduction is not uniquely determined by SRR, but is site- and time-dependent. Factors that may affect the e versus SRR relationship include the structure and size of the sulfate-reducing community, and the nature and accessibility of organic substrates. Whole-sediment data such as those presented here provide a link between isotopic fractionations measured with pure cultures of sulfate-reducing prokaryotes and sulfur isotopic signatures recorded in sedimentary deposits.